Well, as a practical matter, in criminal prosecutions, while you can initially charge both parties, you can only prosecute one party as a defendant and treat the other party as a victim. The school has elected to view your child's actions in the worst possible light and therefor treat your child as the defendant.
Personally, I think that is completely asinine! While "assault" is generally a greater crime than "theft", your child has a right to defend himself and his property. If in the course of recovering his property, he accidentally struck the thief, he should not be punished for it unless it was excesive force, which it doesn't appear to be.
Furthermore, both ADA (Americans with Disability Act) and IDEA (Individuals with Disabilities Education Act) provide extra protections for people with physicial and mental disabilities. Sometimes it may give the school administration pause if they know that you are aware of your son's rights. If I were you, I would send the school a written complaint regarding the incident in question. I would emphasize the thief's role as instigator and that your child's attempt to retrieve his property was a reasonable response, even if he accidentally struck the thief in the process. I would throw in ADA and IDEA, but point out that even without those considerations, the school erred in failing to address the instigator's behavior. I would conclude with the concern that the school is fostering a climate of discrimination and bullying as the "theft" culminated from previous incidents of bullying behavior.
Personally, I would not let the principal off the hook so easily. While she may be able to claim ignorance at the time of the incident and punishment, she is obligated to respond to a written complaint from you. If not, you go up the chain. This will help protect your son should another incident occur.
